1T4E | pdb_00001t4e

Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1T4E/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-04-29 Released: 2005-02-08 
• Deposition Author(s): Grasberger, B.L., Schubert, C., Koblish, H.K., Carver, T.E., Franks, C.F., Zhao, S.Y., Lu, T., LaFrance, L.V., Parks, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells

Grasberger, B.L., Lu, T., Schubert, C., Parks, D.J., Carver, T.E., Koblish, H.K., Cummings, M.D., LaFrance, L.V.

(2005) J Med Chem 48: 909-912

• PubMed: 15715460 
• DOI: https://doi.org/10.1021/jm049137g
• Primary Citation of Related Structures:  
  1T4E, 1T4F


• PubMed Abstract: 
  

  HDM2 binds to an alpha-helical transactivation domain of p53, inhibiting its tumor suppressive functions. A miniaturized thermal denaturation assay was used to screen chemical libraries, resulting in the discovery of a novel series of benzodiazepinedione antagonists of the HDM2-p53 interaction. The X-ray crystal structure of improved antagonists bound to HDM2 reveals their alpha-helix mimetic properties. These optimized molecules increase the transcription of p53 target genes and decrease proliferation of tumor cells expressing wild-type p53.

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research & Development L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.47 kDa 
• Atom Count: 1,682 
• Modeled Residue Count: 192 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-protein ligase E3 Mdm2	A, B	96	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIZ	C [auth A], D [auth B]	(4-CHLOROPHENYL)[3-(4-CHLOROPHENYL)-7-IODO-2,5-DIOXO-1,2,3,5-TETRAHYDRO-4H-1,4-BENZODIAZEPIN-4-YL]ACETIC ACID C23 H15 Cl2 I N2 O4 HQEQUYKKMMKSSX-PMACEKPBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DIZ	BindingDB:  1T4E	Kd: min: 67, max: 80 (nM) from 2 assay(s)
		IC50: min: 200, max: 420 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.240 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.486	α = 90
b = 98.486	β = 90
c = 74.038	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-08 
Deposition Author(s): Grasberger, B.L., Schubert, C., Koblish, H.K., Carver, T.E., Franks, C.F., Zhao, S.Y., Lu, T., LaFrance, L.V., Parks, D.J.

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2018-01-31
  Changes: Experimental preparation
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description